Multiple sequence alignment - TraesCS3A01G230500

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3A01G230500 chr3A 100.000 5711 0 0 1 5711 430774652 430780362 0.000000e+00 10547.0
1 TraesCS3A01G230500 chr3A 90.698 43 4 0 4078 4120 12479746 12479788 2.220000e-04 58.4
2 TraesCS3A01G230500 chr3D 93.822 3804 131 48 677 4436 303594705 303590962 0.000000e+00 5627.0
3 TraesCS3A01G230500 chr3D 92.851 1259 73 9 4466 5711 303590972 303589718 0.000000e+00 1810.0
4 TraesCS3A01G230500 chr3D 89.706 68 6 1 5183 5249 454900240 454900307 1.020000e-12 86.1
5 TraesCS3A01G230500 chr3B 91.451 2632 123 40 713 3293 417712285 417714865 0.000000e+00 3520.0
6 TraesCS3A01G230500 chr3B 95.351 1054 41 5 3393 4444 417714914 417715961 0.000000e+00 1668.0
7 TraesCS3A01G230500 chr3B 92.181 729 34 10 4464 5171 417715947 417716673 0.000000e+00 1009.0
8 TraesCS3A01G230500 chr3B 88.235 68 7 1 5183 5249 597813023 597813090 4.740000e-11 80.5
9 TraesCS3A01G230500 chr3B 95.000 40 2 0 4093 4132 636503193 636503154 4.780000e-06 63.9
10 TraesCS3A01G230500 chr1D 91.204 648 42 11 1 643 489982816 489982179 0.000000e+00 867.0
11 TraesCS3A01G230500 chr1D 91.022 646 46 9 1 639 458720309 458720949 0.000000e+00 861.0
12 TraesCS3A01G230500 chr1D 78.682 516 86 18 3469 3969 478413157 478412651 7.140000e-84 322.0
13 TraesCS3A01G230500 chr1D 79.287 449 88 5 5262 5710 314769006 314769449 5.560000e-80 309.0
14 TraesCS3A01G230500 chr1D 89.189 185 19 1 4491 4675 478412139 478411956 4.450000e-56 230.0
15 TraesCS3A01G230500 chr1D 87.931 116 13 1 1209 1324 478415245 478415131 9.980000e-28 135.0
16 TraesCS3A01G230500 chr1D 87.234 94 11 1 1012 1104 478415405 478415312 7.830000e-19 106.0
17 TraesCS3A01G230500 chr7D 91.149 644 47 7 1 639 568365359 568365997 0.000000e+00 865.0
18 TraesCS3A01G230500 chr5D 90.881 647 49 9 1 643 254593880 254594520 0.000000e+00 859.0
19 TraesCS3A01G230500 chr5D 78.261 299 59 3 5344 5637 302106595 302106892 2.720000e-43 187.0
20 TraesCS3A01G230500 chr4D 90.798 652 47 11 1 647 40799582 40798939 0.000000e+00 859.0
21 TraesCS3A01G230500 chr4D 93.103 58 4 0 1048 1105 12832671 12832728 1.020000e-12 86.1
22 TraesCS3A01G230500 chr2D 90.994 644 47 8 1 639 552574987 552574350 0.000000e+00 857.0
23 TraesCS3A01G230500 chr2D 90.755 649 51 8 1 645 629576932 629577575 0.000000e+00 857.0
24 TraesCS3A01G230500 chr6D 90.615 650 51 8 1 645 55902198 55902842 0.000000e+00 854.0
25 TraesCS3A01G230500 chr6D 90.601 649 50 9 1 645 332951666 332952307 0.000000e+00 850.0
26 TraesCS3A01G230500 chr6D 80.176 454 85 5 5260 5711 16254377 16254827 9.170000e-88 335.0
27 TraesCS3A01G230500 chr6D 77.516 467 85 13 5260 5710 463466184 463466646 4.390000e-66 263.0
28 TraesCS3A01G230500 chr5A 80.685 409 76 3 5296 5703 534944022 534944428 1.190000e-81 315.0
29 TraesCS3A01G230500 chr5A 79.032 372 71 4 5344 5710 395804299 395803930 1.230000e-61 248.0
30 TraesCS3A01G230500 chr6B 78.618 463 81 10 5260 5710 706743075 706743531 2.010000e-74 291.0
31 TraesCS3A01G230500 chr6B 90.141 71 5 2 1048 1116 353789187 353789257 2.190000e-14 91.6
32 TraesCS3A01G230500 chr6B 100.000 33 0 0 673 705 655797823 655797855 1.720000e-05 62.1
33 TraesCS3A01G230500 chrUn 90.395 177 16 1 4499 4675 259903555 259903730 1.240000e-56 231.0
34 TraesCS3A01G230500 chrUn 90.395 177 16 1 4499 4675 437622877 437622702 1.240000e-56 231.0
35 TraesCS3A01G230500 chrUn 89.831 177 17 1 4499 4675 316528927 316529102 5.760000e-55 226.0
36 TraesCS3A01G230500 chrUn 89.831 177 17 1 4499 4675 357960524 357960349 5.760000e-55 226.0
37 TraesCS3A01G230500 chr1A 89.944 179 17 1 4497 4675 574666017 574665840 4.450000e-56 230.0
38 TraesCS3A01G230500 chr1A 86.256 211 27 2 3472 3681 574667037 574666828 1.600000e-55 228.0
39 TraesCS3A01G230500 chr1A 85.600 125 16 2 1201 1324 574669170 574669047 4.640000e-26 130.0
40 TraesCS3A01G230500 chr1A 90.110 91 5 4 1019 1109 574669310 574669224 1.300000e-21 115.0
41 TraesCS3A01G230500 chr1B 87.310 197 24 1 4474 4670 666536211 666536016 2.070000e-54 224.0
42 TraesCS3A01G230500 chr1B 88.136 118 14 0 1207 1324 666538973 666538856 2.150000e-29 141.0
43 TraesCS3A01G230500 chr1B 87.129 101 9 4 1019 1116 666539113 666539014 1.680000e-20 111.0
44 TraesCS3A01G230500 chr5B 78.543 247 49 3 5465 5710 345323553 345323796 5.920000e-35 159.0
45 TraesCS3A01G230500 chr5B 91.667 48 1 1 673 720 357414839 357414795 4.780000e-06 63.9
46 TraesCS3A01G230500 chr2B 84.112 107 17 0 1218 1324 703573548 703573654 2.810000e-18 104.0
47 TraesCS3A01G230500 chr2B 90.141 71 5 2 1048 1116 703573481 703573551 2.190000e-14 91.6
48 TraesCS3A01G230500 chr2B 82.432 74 11 2 4060 4132 59765491 59765563 4.780000e-06 63.9
49 TraesCS3A01G230500 chr7A 88.732 71 6 2 1048 1116 337923175 337923245 1.020000e-12 86.1
50 TraesCS3A01G230500 chr4B 86.957 69 9 0 1256 1324 509256580 509256648 1.710000e-10 78.7
51 TraesCS3A01G230500 chr4A 89.796 49 2 1 673 721 37785991 37785946 6.180000e-05 60.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G230500 chr3A 430774652 430780362 5710 False 10547.000000 10547 100.000000 1 5711 1 chr3A.!!$F2 5710
1 TraesCS3A01G230500 chr3D 303589718 303594705 4987 True 3718.500000 5627 93.336500 677 5711 2 chr3D.!!$R1 5034
2 TraesCS3A01G230500 chr3B 417712285 417716673 4388 False 2065.666667 3520 92.994333 713 5171 3 chr3B.!!$F2 4458
3 TraesCS3A01G230500 chr1D 489982179 489982816 637 True 867.000000 867 91.204000 1 643 1 chr1D.!!$R1 642
4 TraesCS3A01G230500 chr1D 458720309 458720949 640 False 861.000000 861 91.022000 1 639 1 chr1D.!!$F2 638
5 TraesCS3A01G230500 chr7D 568365359 568365997 638 False 865.000000 865 91.149000 1 639 1 chr7D.!!$F1 638
6 TraesCS3A01G230500 chr5D 254593880 254594520 640 False 859.000000 859 90.881000 1 643 1 chr5D.!!$F1 642
7 TraesCS3A01G230500 chr4D 40798939 40799582 643 True 859.000000 859 90.798000 1 647 1 chr4D.!!$R1 646
8 TraesCS3A01G230500 chr2D 552574350 552574987 637 True 857.000000 857 90.994000 1 639 1 chr2D.!!$R1 638
9 TraesCS3A01G230500 chr2D 629576932 629577575 643 False 857.000000 857 90.755000 1 645 1 chr2D.!!$F1 644
10 TraesCS3A01G230500 chr6D 55902198 55902842 644 False 854.000000 854 90.615000 1 645 1 chr6D.!!$F2 644
11 TraesCS3A01G230500 chr6D 332951666 332952307 641 False 850.000000 850 90.601000 1 645 1 chr6D.!!$F3 644

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
423 432 0.040514 TCTGCGTGCGTGAAAATTGG 60.041 50.0 0.00 0.00 0.00 3.16 F
493 504 0.256464 AAAAAGGACGTGTGGGTGGA 59.744 50.0 0.00 0.00 0.00 4.02 F
2193 2242 0.757935 ATCACATTCCATGGCTGGCC 60.758 55.0 6.96 4.43 42.80 5.36 F
2492 2554 0.257039 ACCTGCCATGTCTCAATCCC 59.743 55.0 0.00 0.00 0.00 3.85 F
2641 2703 0.381801 CAGCGTTTGCACAAGAGGTT 59.618 50.0 0.00 0.00 46.23 3.50 F
4053 4149 0.383949 TTGTTTCGCCTTTGGAGCAC 59.616 50.0 0.00 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 1926 3.406764 GTGAGAGAGTGCAAAACCAGAT 58.593 45.455 0.00 0.00 0.00 2.90 R
2473 2523 0.257039 GGGATTGAGACATGGCAGGT 59.743 55.000 3.63 3.63 0.00 4.00 R
4172 4269 0.463654 TAAGCCATCGTGATGCCACC 60.464 55.000 4.29 0.00 40.12 4.61 R
4490 4588 0.604780 CCTCAGGTTCTGCACACCAG 60.605 60.000 12.05 5.00 43.17 4.00 R
4539 4637 0.109597 GCTTCATCACGTTGGCCAAG 60.110 55.000 21.21 15.48 0.00 3.61 R
5089 5209 0.034756 TGCATGTTACCAGACACGCT 59.965 50.000 0.00 0.00 39.31 5.07 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.089920 GTCTACTGCAGTTGCCATGG 58.910 55.000 27.06 7.63 41.18 3.66
61 62 6.710295 GGTTTCAAAATTTTAGGAGTTGCCAT 59.290 34.615 2.44 0.00 40.02 4.40
82 83 2.969950 TCCACTAACACTAGGCAGTTGT 59.030 45.455 7.49 0.00 30.46 3.32
84 85 2.987149 CACTAACACTAGGCAGTTGTCG 59.013 50.000 7.49 0.00 30.46 4.35
95 96 2.400399 GCAGTTGTCGTGTAGCACTAA 58.600 47.619 0.00 0.00 31.34 2.24
140 145 6.585695 TGTACGGATAAAAGAGAGAGTTGT 57.414 37.500 0.00 0.00 0.00 3.32
141 146 6.989659 TGTACGGATAAAAGAGAGAGTTGTT 58.010 36.000 0.00 0.00 0.00 2.83
142 147 6.866770 TGTACGGATAAAAGAGAGAGTTGTTG 59.133 38.462 0.00 0.00 0.00 3.33
215 221 0.456142 CTGCTTACGTGCACGCTAGA 60.456 55.000 37.35 18.49 44.43 2.43
260 268 3.637911 AAATACATGGCAACTCGGGTA 57.362 42.857 0.00 0.00 37.61 3.69
361 370 3.083997 GGGTGTGGGCGAGGAGAT 61.084 66.667 0.00 0.00 0.00 2.75
423 432 0.040514 TCTGCGTGCGTGAAAATTGG 60.041 50.000 0.00 0.00 0.00 3.16
424 433 0.317770 CTGCGTGCGTGAAAATTGGT 60.318 50.000 0.00 0.00 0.00 3.67
441 450 1.452145 GGTGTGTGTGGGCGAATTGT 61.452 55.000 0.00 0.00 0.00 2.71
490 501 1.385528 GTGAAAAAGGACGTGTGGGT 58.614 50.000 0.00 0.00 0.00 4.51
492 503 0.666374 GAAAAAGGACGTGTGGGTGG 59.334 55.000 0.00 0.00 0.00 4.61
493 504 0.256464 AAAAAGGACGTGTGGGTGGA 59.744 50.000 0.00 0.00 0.00 4.02
495 506 1.354101 AAAGGACGTGTGGGTGGATA 58.646 50.000 0.00 0.00 0.00 2.59
503 514 3.964688 ACGTGTGGGTGGATAGATGAATA 59.035 43.478 0.00 0.00 0.00 1.75
506 518 4.348168 GTGTGGGTGGATAGATGAATACCT 59.652 45.833 0.00 0.00 0.00 3.08
526 538 2.826128 CTCACACCAGCTTAGTCCTACA 59.174 50.000 0.00 0.00 0.00 2.74
584 598 3.306019 GCAAAATTGGTTGGACGAGGATT 60.306 43.478 0.00 0.00 0.00 3.01
588 602 3.433306 TTGGTTGGACGAGGATTCATT 57.567 42.857 0.00 0.00 0.00 2.57
645 659 5.214417 GGGCGTTAGTGTTTTCGTAAAAAT 58.786 37.500 0.00 0.00 36.77 1.82
646 660 6.017605 TGGGCGTTAGTGTTTTCGTAAAAATA 60.018 34.615 0.00 0.00 36.77 1.40
647 661 7.022979 GGGCGTTAGTGTTTTCGTAAAAATAT 58.977 34.615 0.00 0.00 36.77 1.28
648 662 7.007636 GGGCGTTAGTGTTTTCGTAAAAATATG 59.992 37.037 0.00 0.00 36.77 1.78
649 663 7.745594 GGCGTTAGTGTTTTCGTAAAAATATGA 59.254 33.333 0.00 0.00 36.77 2.15
650 664 9.269415 GCGTTAGTGTTTTCGTAAAAATATGAT 57.731 29.630 0.00 0.00 36.77 2.45
654 668 8.816204 AGTGTTTTCGTAAAAATATGATACGC 57.184 30.769 9.24 0.00 41.49 4.42
655 669 7.906527 AGTGTTTTCGTAAAAATATGATACGCC 59.093 33.333 9.24 1.61 41.49 5.68
656 670 6.900828 TGTTTTCGTAAAAATATGATACGCCG 59.099 34.615 9.24 0.00 41.49 6.46
657 671 6.586868 TTTCGTAAAAATATGATACGCCGT 57.413 33.333 0.00 0.00 41.49 5.68
658 672 6.586868 TTCGTAAAAATATGATACGCCGTT 57.413 33.333 0.00 0.00 41.49 4.44
659 673 5.965202 TCGTAAAAATATGATACGCCGTTG 58.035 37.500 0.00 0.00 41.49 4.10
660 674 5.747675 TCGTAAAAATATGATACGCCGTTGA 59.252 36.000 0.00 0.00 41.49 3.18
661 675 5.837191 CGTAAAAATATGATACGCCGTTGAC 59.163 40.000 0.00 0.00 36.41 3.18
662 676 4.446857 AAAATATGATACGCCGTTGACG 57.553 40.909 0.00 0.00 39.44 4.35
669 683 2.634982 TACGCCGTTGACGTATTCTT 57.365 45.000 0.00 0.00 44.55 2.52
670 684 1.065358 ACGCCGTTGACGTATTCTTG 58.935 50.000 2.63 0.00 43.02 3.02
671 685 1.336148 ACGCCGTTGACGTATTCTTGA 60.336 47.619 2.63 0.00 43.02 3.02
672 686 1.722464 CGCCGTTGACGTATTCTTGAA 59.278 47.619 2.63 0.00 37.74 2.69
673 687 2.156117 CGCCGTTGACGTATTCTTGAAA 59.844 45.455 2.63 0.00 37.74 2.69
674 688 3.363182 CGCCGTTGACGTATTCTTGAAAA 60.363 43.478 2.63 0.00 37.74 2.29
675 689 4.529446 GCCGTTGACGTATTCTTGAAAAA 58.471 39.130 2.63 0.00 37.74 1.94
676 690 5.151389 GCCGTTGACGTATTCTTGAAAAAT 58.849 37.500 2.63 0.00 37.74 1.82
677 691 6.308675 GCCGTTGACGTATTCTTGAAAAATA 58.691 36.000 2.63 0.00 37.74 1.40
678 692 6.797995 GCCGTTGACGTATTCTTGAAAAATAA 59.202 34.615 2.63 0.00 37.74 1.40
679 693 7.483691 GCCGTTGACGTATTCTTGAAAAATAAT 59.516 33.333 2.63 0.00 37.74 1.28
680 694 9.976255 CCGTTGACGTATTCTTGAAAAATAATA 57.024 29.630 2.63 0.00 37.74 0.98
908 929 1.025113 TCCACAGACTACTCCTCGCG 61.025 60.000 0.00 0.00 0.00 5.87
1230 1251 2.760385 CGGGAGGACTGGGAGGTC 60.760 72.222 0.00 0.00 35.66 3.85
1353 1374 4.437390 CCATCTCAACTTCACATTTACGCC 60.437 45.833 0.00 0.00 0.00 5.68
1505 1526 5.413523 GCTTCTTTATTTTTCTCCCCGTACA 59.586 40.000 0.00 0.00 0.00 2.90
1555 1576 3.986572 GCAGAATGAGTTGATCGATCGAT 59.013 43.478 29.76 29.76 39.69 3.59
1902 1926 1.627329 AGAAGCATCTGAGCCAGAACA 59.373 47.619 8.66 0.00 44.04 3.18
2083 2125 6.760298 TCATAAAATGCAACTTGTCAAAGCAA 59.240 30.769 10.03 0.00 38.85 3.91
2110 2152 9.569167 TTACTAACTCATTGAAGTTATCGACTG 57.431 33.333 0.00 2.02 40.12 3.51
2134 2176 4.214758 GCTCGTTTTGCCCTTTTTCTACTA 59.785 41.667 0.00 0.00 0.00 1.82
2170 2219 5.666969 TGAAACCAGTGAATAGTTTGTCG 57.333 39.130 0.00 0.00 34.00 4.35
2193 2242 0.757935 ATCACATTCCATGGCTGGCC 60.758 55.000 6.96 4.43 42.80 5.36
2386 2436 5.104776 AGCCAATACTCTTCTCAATGCACTA 60.105 40.000 0.00 0.00 0.00 2.74
2389 2439 7.201767 GCCAATACTCTTCTCAATGCACTAAAT 60.202 37.037 0.00 0.00 0.00 1.40
2436 2486 2.441750 ACCTTTGGTCCTTAGCAACTGA 59.558 45.455 0.00 0.00 42.54 3.41
2440 2490 5.123979 CCTTTGGTCCTTAGCAACTGATAAC 59.876 44.000 0.00 0.00 42.54 1.89
2490 2552 5.615289 AGTATAACCTGCCATGTCTCAATC 58.385 41.667 0.00 0.00 0.00 2.67
2491 2553 2.134789 AACCTGCCATGTCTCAATCC 57.865 50.000 0.00 0.00 0.00 3.01
2492 2554 0.257039 ACCTGCCATGTCTCAATCCC 59.743 55.000 0.00 0.00 0.00 3.85
2493 2555 0.549950 CCTGCCATGTCTCAATCCCT 59.450 55.000 0.00 0.00 0.00 4.20
2494 2556 1.476471 CCTGCCATGTCTCAATCCCTC 60.476 57.143 0.00 0.00 0.00 4.30
2502 2564 4.038271 TGTCTCAATCCCTCTGCAAAAT 57.962 40.909 0.00 0.00 0.00 1.82
2507 2569 7.178983 TGTCTCAATCCCTCTGCAAAATTAAAT 59.821 33.333 0.00 0.00 0.00 1.40
2611 2673 8.543774 GGTCATAGATCAGAACAAGAAATTACG 58.456 37.037 0.00 0.00 0.00 3.18
2626 2688 2.203800 TTACGGCACTAAGATCAGCG 57.796 50.000 0.00 0.00 0.00 5.18
2641 2703 0.381801 CAGCGTTTGCACAAGAGGTT 59.618 50.000 0.00 0.00 46.23 3.50
2705 2767 2.234143 GCTTTGGCTGAAGAAGTCCTT 58.766 47.619 5.56 0.00 34.96 3.36
2715 2777 1.677966 GAAGTCCTTTTCCCGCCCC 60.678 63.158 0.00 0.00 0.00 5.80
2718 2780 1.228769 GTCCTTTTCCCGCCCCTTT 60.229 57.895 0.00 0.00 0.00 3.11
2719 2781 1.076014 TCCTTTTCCCGCCCCTTTC 59.924 57.895 0.00 0.00 0.00 2.62
2722 2784 1.044611 CTTTTCCCGCCCCTTTCAAA 58.955 50.000 0.00 0.00 0.00 2.69
2723 2785 1.414550 CTTTTCCCGCCCCTTTCAAAA 59.585 47.619 0.00 0.00 0.00 2.44
2807 2869 5.245751 TCATAAAACAATGACTGCATGGGTT 59.754 36.000 0.00 0.00 36.93 4.11
2839 2901 4.222124 AGTGTTCTCCAATATGGTCCAC 57.778 45.455 0.00 0.61 39.03 4.02
2884 2947 6.315144 TCCTTTTAACATACACGATCCACATG 59.685 38.462 0.00 0.00 0.00 3.21
2898 2961 5.237127 CGATCCACATGCTACAACAATATGT 59.763 40.000 0.00 0.00 37.32 2.29
2927 2990 1.080638 TGGCCAGTTATCCCTTTGGT 58.919 50.000 0.00 0.00 33.21 3.67
2940 3003 2.556622 CCCTTTGGTGTCGCTTATGTTT 59.443 45.455 0.00 0.00 0.00 2.83
3030 3093 7.020914 AGTTGACTATTGCTAGCTATTTTGC 57.979 36.000 16.77 5.71 0.00 3.68
3088 3153 7.729116 AGTTCCATAATTTATTCAAGGCATGG 58.271 34.615 0.00 0.00 34.32 3.66
3163 3229 9.685828 CCGTAAAAGAAGTTCCATAATTTTTCA 57.314 29.630 0.00 0.00 0.00 2.69
3175 3241 6.210584 TCCATAATTTTTCACTTCTTGACCCC 59.789 38.462 0.00 0.00 32.26 4.95
3176 3242 6.211384 CCATAATTTTTCACTTCTTGACCCCT 59.789 38.462 0.00 0.00 32.26 4.79
3177 3243 5.535753 AATTTTTCACTTCTTGACCCCTG 57.464 39.130 0.00 0.00 32.26 4.45
3245 3312 9.139174 ACTTTGTCAACACTAGTGAAAAATTTG 57.861 29.630 29.30 19.93 0.00 2.32
3246 3313 8.472683 TTTGTCAACACTAGTGAAAAATTTGG 57.527 30.769 29.30 2.61 0.00 3.28
3247 3314 7.164230 TGTCAACACTAGTGAAAAATTTGGT 57.836 32.000 29.30 0.00 0.00 3.67
3248 3315 7.607250 TGTCAACACTAGTGAAAAATTTGGTT 58.393 30.769 29.30 6.07 0.00 3.67
3249 3316 8.091449 TGTCAACACTAGTGAAAAATTTGGTTT 58.909 29.630 29.30 5.54 0.00 3.27
3250 3317 9.575783 GTCAACACTAGTGAAAAATTTGGTTTA 57.424 29.630 29.30 3.69 0.00 2.01
3251 3318 9.796120 TCAACACTAGTGAAAAATTTGGTTTAG 57.204 29.630 29.30 4.32 0.00 1.85
3552 3647 3.664107 TCTTGGCATGCCGAGTAATATC 58.336 45.455 40.66 13.97 45.63 1.63
3558 3653 3.657634 CATGCCGAGTAATATCTGCTGT 58.342 45.455 0.00 0.00 31.42 4.40
3738 3833 6.702282 CGAAGTTCTTCTATTATGTCCCTTCC 59.298 42.308 10.24 0.00 0.00 3.46
3760 3855 2.205022 TTGGGAAGGTCTCATTGCTG 57.795 50.000 0.00 0.00 0.00 4.41
3767 3862 2.716217 AGGTCTCATTGCTGCCTTTAC 58.284 47.619 0.00 0.00 0.00 2.01
4020 4116 5.957771 TCAGATATGTCTTAAGTTGGGCT 57.042 39.130 1.63 0.00 30.42 5.19
4053 4149 0.383949 TTGTTTCGCCTTTGGAGCAC 59.616 50.000 0.00 0.00 0.00 4.40
4074 4170 5.636123 CACTGGATAGTACTACCTCCATCT 58.364 45.833 20.60 9.97 37.18 2.90
4091 4187 8.701895 ACCTCCATCTGATATTAGTTTTCGTTA 58.298 33.333 0.00 0.00 0.00 3.18
4158 4255 2.364324 GAGCGACCACTAATATGGGACA 59.636 50.000 0.00 0.00 44.81 4.02
4170 4267 2.680352 GGGACAGAGGGAGCGTGA 60.680 66.667 0.00 0.00 0.00 4.35
4172 4269 1.142748 GGACAGAGGGAGCGTGATG 59.857 63.158 0.00 0.00 0.00 3.07
4263 4360 6.374333 ACAACAGGAAATGCGATGTTTATAGT 59.626 34.615 0.00 0.00 33.76 2.12
4269 4366 7.122055 AGGAAATGCGATGTTTATAGTTTTGGA 59.878 33.333 0.00 0.00 0.00 3.53
4386 4484 1.455383 CCTTTCCTTGTGGCGTTGCT 61.455 55.000 0.00 0.00 0.00 3.91
4408 4506 1.795286 GGCTCTTGTTTCTGACGTCTG 59.205 52.381 17.92 16.72 0.00 3.51
4409 4507 2.545952 GGCTCTTGTTTCTGACGTCTGA 60.546 50.000 19.81 19.81 0.00 3.27
4410 4508 3.123804 GCTCTTGTTTCTGACGTCTGAA 58.876 45.455 27.72 27.72 33.02 3.02
4411 4509 3.183373 GCTCTTGTTTCTGACGTCTGAAG 59.817 47.826 28.98 20.97 35.68 3.02
4432 4530 4.062991 AGTCTGAACCACCGAAAACATAC 58.937 43.478 0.00 0.00 0.00 2.39
4433 4531 3.810941 GTCTGAACCACCGAAAACATACA 59.189 43.478 0.00 0.00 0.00 2.29
4434 4532 4.454504 GTCTGAACCACCGAAAACATACAT 59.545 41.667 0.00 0.00 0.00 2.29
4435 4533 5.640357 GTCTGAACCACCGAAAACATACATA 59.360 40.000 0.00 0.00 0.00 2.29
4436 4534 6.315393 GTCTGAACCACCGAAAACATACATAT 59.685 38.462 0.00 0.00 0.00 1.78
4437 4535 7.493320 GTCTGAACCACCGAAAACATACATATA 59.507 37.037 0.00 0.00 0.00 0.86
4438 4536 8.208224 TCTGAACCACCGAAAACATACATATAT 58.792 33.333 0.00 0.00 0.00 0.86
4439 4537 8.740123 TGAACCACCGAAAACATACATATATT 57.260 30.769 0.00 0.00 0.00 1.28
4440 4538 9.833917 TGAACCACCGAAAACATACATATATTA 57.166 29.630 0.00 0.00 0.00 0.98
4457 4555 9.381038 ACATATATTATACTCCTTGTGGACTGT 57.619 33.333 0.00 0.00 37.46 3.55
4458 4556 9.645059 CATATATTATACTCCTTGTGGACTGTG 57.355 37.037 0.00 0.00 37.46 3.66
4459 4557 4.819105 TTATACTCCTTGTGGACTGTGG 57.181 45.455 0.00 0.00 37.46 4.17
4460 4558 2.391926 TACTCCTTGTGGACTGTGGA 57.608 50.000 0.00 0.00 37.46 4.02
4461 4559 1.051812 ACTCCTTGTGGACTGTGGAG 58.948 55.000 7.77 7.77 46.93 3.86
4462 4560 1.051812 CTCCTTGTGGACTGTGGAGT 58.948 55.000 0.00 0.00 39.39 3.85
4463 4561 2.248248 CTCCTTGTGGACTGTGGAGTA 58.752 52.381 0.00 0.00 39.39 2.59
4464 4562 2.834549 CTCCTTGTGGACTGTGGAGTAT 59.165 50.000 0.00 0.00 39.39 2.12
4465 4563 4.023980 CTCCTTGTGGACTGTGGAGTATA 58.976 47.826 0.00 0.00 39.39 1.47
4557 4655 0.523072 CCTTGGCCAACGTGATGAAG 59.477 55.000 16.05 0.38 0.00 3.02
4731 4829 3.733960 TCTGGTCTGACGGCGTCG 61.734 66.667 31.90 25.60 43.02 5.12
4797 4907 4.689071 TGTCGGTTATGGCTAATGTAGTG 58.311 43.478 0.00 0.00 0.00 2.74
4810 4920 0.739462 TGTAGTGAATGCCCGCTTCG 60.739 55.000 0.00 0.00 0.00 3.79
4873 4983 1.478288 GCATGCCCTAGGATCAAGCTT 60.478 52.381 11.48 0.00 0.00 3.74
4888 4999 3.815401 TCAAGCTTGGAGTTTAGTTGAGC 59.185 43.478 25.73 0.00 0.00 4.26
4966 5078 9.098355 ACACACTGTACTATTGCAGTTTATATG 57.902 33.333 0.97 0.00 45.55 1.78
5089 5209 4.689071 AGTGTTCGTCTGTGTTGTATTGA 58.311 39.130 0.00 0.00 0.00 2.57
5096 5216 3.057019 TCTGTGTTGTATTGAGCGTGTC 58.943 45.455 0.00 0.00 0.00 3.67
5142 5262 5.630539 GCCCCCTAACATATGTGTTTGTCTA 60.631 44.000 13.37 0.00 46.07 2.59
5175 5295 0.957395 CTGGCTGCGAGGAAACACAT 60.957 55.000 3.49 0.00 0.00 3.21
5196 5316 1.679305 ACGGTGGTGTTTGGTTGCA 60.679 52.632 0.00 0.00 0.00 4.08
5198 5318 1.380403 CGGTGGTGTTTGGTTGCAGA 61.380 55.000 0.00 0.00 0.00 4.26
5204 5324 2.094234 GGTGTTTGGTTGCAGACTTGTT 60.094 45.455 0.00 0.00 0.00 2.83
5205 5325 3.179048 GTGTTTGGTTGCAGACTTGTTC 58.821 45.455 0.00 0.00 0.00 3.18
5206 5326 3.088532 TGTTTGGTTGCAGACTTGTTCT 58.911 40.909 0.00 0.00 33.33 3.01
5207 5327 4.095782 GTGTTTGGTTGCAGACTTGTTCTA 59.904 41.667 0.00 0.00 31.12 2.10
5221 5341 5.551233 ACTTGTTCTAGCAGATGCAAAGTA 58.449 37.500 7.68 0.00 45.16 2.24
5226 5346 4.445453 TCTAGCAGATGCAAAGTATGTGG 58.555 43.478 7.68 0.00 45.16 4.17
5306 5426 4.222145 ACTCATAAGCCGGAGTCTTAAACA 59.778 41.667 5.05 0.00 40.18 2.83
5309 5429 2.165319 AGCCGGAGTCTTAAACACAC 57.835 50.000 5.05 0.00 0.00 3.82
5330 5450 7.012515 ACACACAGTTAAACGATAAAATGGTCA 59.987 33.333 0.00 0.00 0.00 4.02
5339 5459 3.119990 CGATAAAATGGTCACGGCAAAGT 60.120 43.478 0.00 0.00 0.00 2.66
5379 5499 6.317391 GCAAAAGTCTTAGGTGCAGAGATAAT 59.683 38.462 9.73 0.00 35.28 1.28
5436 5556 0.033601 TTGCACTTGGTCACCACCTT 60.034 50.000 0.00 0.00 44.17 3.50
5448 5568 0.038526 ACCACCTTGACATCGTCGTC 60.039 55.000 0.00 0.81 34.95 4.20
5508 5628 0.899720 TTGATGGTGACGAGGTACCC 59.100 55.000 8.74 0.00 36.10 3.69
5510 5630 2.012902 GATGGTGACGAGGTACCCGG 62.013 65.000 21.70 11.89 36.10 5.73
5519 5639 1.777941 GAGGTACCCGGTCTTGATCT 58.222 55.000 8.74 0.00 0.00 2.75
5561 5681 2.093341 GGCCTACCCTTATCAAACACGA 60.093 50.000 0.00 0.00 0.00 4.35
5564 5684 2.109425 ACCCTTATCAAACACGAGCC 57.891 50.000 0.00 0.00 0.00 4.70
5567 5687 1.398390 CCTTATCAAACACGAGCCTGC 59.602 52.381 0.00 0.00 0.00 4.85
5568 5688 1.398390 CTTATCAAACACGAGCCTGCC 59.602 52.381 0.00 0.00 0.00 4.85
5569 5689 0.323302 TATCAAACACGAGCCTGCCA 59.677 50.000 0.00 0.00 0.00 4.92
5579 5699 1.542767 CGAGCCTGCCATTGATCATCT 60.543 52.381 0.00 0.00 0.00 2.90
5593 5713 2.526888 TCATCTAGACCGTCACCCTT 57.473 50.000 0.00 0.00 0.00 3.95
5602 5722 1.153823 CGTCACCCTTCAGGCGTAG 60.154 63.158 0.00 0.00 40.58 3.51
5620 5740 1.210155 GCCGGTGTTTGTCATCAGC 59.790 57.895 1.90 0.00 0.00 4.26
5633 5753 4.259356 TGTCATCAGCTTGAATTCCTCTG 58.741 43.478 2.27 7.55 0.00 3.35
5638 5758 1.988107 AGCTTGAATTCCTCTGGGACA 59.012 47.619 2.27 0.00 42.05 4.02
5639 5759 2.376518 AGCTTGAATTCCTCTGGGACAA 59.623 45.455 2.27 0.00 42.05 3.18
5665 5785 3.565482 TGAAGTGATTGGTGAACTCAAGC 59.435 43.478 0.00 0.00 0.00 4.01
5666 5786 2.146342 AGTGATTGGTGAACTCAAGCG 58.854 47.619 0.00 0.00 33.72 4.68
5671 5791 2.254546 TGGTGAACTCAAGCGACATT 57.745 45.000 0.00 0.00 0.00 2.71
5685 5805 1.303888 ACATTGGCAGGCACTCCAG 60.304 57.895 0.00 0.00 37.08 3.86
5687 5807 0.896940 CATTGGCAGGCACTCCAGTT 60.897 55.000 0.00 0.00 37.08 3.16
5691 5811 1.228245 GCAGGCACTCCAGTTTGGA 60.228 57.895 0.00 0.00 45.98 3.53
5703 5823 2.165030 CCAGTTTGGATGCAAGGATGAC 59.835 50.000 0.00 0.00 40.96 3.06
5704 5824 2.821378 CAGTTTGGATGCAAGGATGACA 59.179 45.455 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.760650 TGCAGTAGACCAGACCATACAG 59.239 50.000 0.00 0.00 0.00 2.74
37 38 7.095229 GGATGGCAACTCCTAAAATTTTGAAAC 60.095 37.037 13.76 0.00 35.26 2.78
61 62 2.969950 ACAACTGCCTAGTGTTAGTGGA 59.030 45.455 0.00 0.00 37.19 4.02
120 125 5.696724 CACAACAACTCTCTCTTTTATCCGT 59.303 40.000 0.00 0.00 0.00 4.69
124 129 6.058183 AGCACACAACAACTCTCTCTTTTAT 58.942 36.000 0.00 0.00 0.00 1.40
241 249 3.637911 TTACCCGAGTTGCCATGTATT 57.362 42.857 0.00 0.00 0.00 1.89
245 253 2.817258 TCTTTTTACCCGAGTTGCCATG 59.183 45.455 0.00 0.00 0.00 3.66
246 254 3.149005 TCTTTTTACCCGAGTTGCCAT 57.851 42.857 0.00 0.00 0.00 4.40
297 306 0.608856 CAGGGTACATGGCAACTGCA 60.609 55.000 3.76 0.00 44.36 4.41
340 349 2.035626 CCTCGCCCACACCCAAAT 59.964 61.111 0.00 0.00 0.00 2.32
423 432 0.383949 AACAATTCGCCCACACACAC 59.616 50.000 0.00 0.00 0.00 3.82
424 433 1.968704 TAACAATTCGCCCACACACA 58.031 45.000 0.00 0.00 0.00 3.72
441 450 1.448922 GCTGGTGTGTGGGCGTTTAA 61.449 55.000 0.00 0.00 0.00 1.52
490 501 5.215845 TGGTGTGAGGTATTCATCTATCCA 58.784 41.667 0.00 0.00 38.29 3.41
492 503 5.011533 AGCTGGTGTGAGGTATTCATCTATC 59.988 44.000 0.00 0.00 38.29 2.08
493 504 4.904251 AGCTGGTGTGAGGTATTCATCTAT 59.096 41.667 0.00 0.00 38.29 1.98
495 506 3.110705 AGCTGGTGTGAGGTATTCATCT 58.889 45.455 0.00 0.00 38.29 2.90
503 514 0.977395 GGACTAAGCTGGTGTGAGGT 59.023 55.000 0.00 0.00 0.00 3.85
506 518 2.884320 TGTAGGACTAAGCTGGTGTGA 58.116 47.619 0.00 0.00 0.00 3.58
534 546 3.131400 TCTTGGTGCGTTTTAGCCTTTTT 59.869 39.130 0.00 0.00 36.02 1.94
550 564 5.231702 ACCAATTTTGCATGAATCTTGGT 57.768 34.783 12.23 12.23 0.00 3.67
584 598 0.948623 CAACTCGCCCACACGAATGA 60.949 55.000 0.00 0.00 42.39 2.57
650 664 2.095314 TCAAGAATACGTCAACGGCGTA 60.095 45.455 15.20 3.08 46.63 4.42
651 665 1.065358 CAAGAATACGTCAACGGCGT 58.935 50.000 6.77 6.77 44.95 5.68
652 666 1.342555 TCAAGAATACGTCAACGGCG 58.657 50.000 4.80 4.80 44.95 6.46
653 667 3.799137 TTTCAAGAATACGTCAACGGC 57.201 42.857 7.53 0.00 44.95 5.68
654 668 8.889849 ATTATTTTTCAAGAATACGTCAACGG 57.110 30.769 7.53 0.00 44.95 4.44
705 719 1.483415 GGCATGTACTCCCTCCGTAAA 59.517 52.381 0.00 0.00 0.00 2.01
710 724 0.181350 CCTTGGCATGTACTCCCTCC 59.819 60.000 0.00 0.00 0.00 4.30
1215 1236 2.053277 GTCGACCTCCCAGTCCTCC 61.053 68.421 3.51 0.00 32.91 4.30
1353 1374 5.617751 GCACTGAAATTGGCAAGTAGTGTAG 60.618 44.000 23.56 11.52 37.11 2.74
1902 1926 3.406764 GTGAGAGAGTGCAAAACCAGAT 58.593 45.455 0.00 0.00 0.00 2.90
2170 2219 3.996150 CAGCCATGGAATGTGATAACC 57.004 47.619 18.40 0.00 44.81 2.85
2193 2242 4.081862 ACAATGGCAGATTCAAATGTCTGG 60.082 41.667 0.00 0.00 41.62 3.86
2327 2377 9.139174 GAACAACAAGTCTTTGAAGAAAATTCA 57.861 29.630 0.00 0.00 36.68 2.57
2328 2378 9.139174 TGAACAACAAGTCTTTGAAGAAAATTC 57.861 29.630 0.00 0.00 36.68 2.17
2348 2398 4.826733 AGTATTGGCTGTCATGTTGAACAA 59.173 37.500 0.62 0.00 0.00 2.83
2386 2436 7.906010 CGCATTATTCATGAACAAAATGCATTT 59.094 29.630 35.05 18.99 34.31 2.32
2389 2439 5.868258 ACGCATTATTCATGAACAAAATGCA 59.132 32.000 35.05 11.33 34.31 3.96
2440 2490 8.616076 AGCGAAATTCAAATCTCAAATAGTAGG 58.384 33.333 0.00 0.00 0.00 3.18
2473 2523 0.257039 GGGATTGAGACATGGCAGGT 59.743 55.000 3.63 3.63 0.00 4.00
2552 2614 3.567164 CAGTCAAGCAACTTCACTGGAAT 59.433 43.478 3.69 0.00 38.58 3.01
2611 2673 1.202076 GCAAACGCTGATCTTAGTGCC 60.202 52.381 0.00 0.00 0.00 5.01
2626 2688 1.134946 ACAGCAACCTCTTGTGCAAAC 59.865 47.619 0.00 0.00 0.00 2.93
2705 2767 1.723288 ATTTTGAAAGGGGCGGGAAA 58.277 45.000 0.00 0.00 0.00 3.13
2780 2842 6.819649 CCCATGCAGTCATTGTTTTATGAAAT 59.180 34.615 0.00 0.00 36.37 2.17
2802 2864 3.222173 ACACTTTCAGCATGTAACCCA 57.778 42.857 0.00 0.00 37.40 4.51
2803 2865 3.821033 AGAACACTTTCAGCATGTAACCC 59.179 43.478 0.00 0.00 37.40 4.11
2807 2869 4.350368 TGGAGAACACTTTCAGCATGTA 57.650 40.909 0.00 0.00 37.40 2.29
2839 2901 0.033208 AGGTTGCCCATGTGGTATGG 60.033 55.000 0.00 0.00 38.88 2.74
2860 2923 6.486248 CATGTGGATCGTGTATGTTAAAAGG 58.514 40.000 0.00 0.00 0.00 3.11
2861 2924 5.965334 GCATGTGGATCGTGTATGTTAAAAG 59.035 40.000 0.00 0.00 35.64 2.27
2871 2934 2.289382 TGTTGTAGCATGTGGATCGTGT 60.289 45.455 0.00 0.00 35.64 4.49
2898 2961 4.892934 GGGATAACTGGCCACATAATTCAA 59.107 41.667 0.00 0.00 0.00 2.69
3030 3093 6.089551 CGGGAATTATATGACAACTAAGAGCG 59.910 42.308 0.00 0.00 0.00 5.03
3088 3153 8.638685 AAGCATGTAAACTTTGATAATGATGC 57.361 30.769 0.00 0.00 34.12 3.91
3163 3229 1.417890 CTGTGTCAGGGGTCAAGAAGT 59.582 52.381 0.00 0.00 0.00 3.01
3175 3241 6.260936 ACAAAGGTTCTAATGTTCTGTGTCAG 59.739 38.462 0.00 0.00 0.00 3.51
3176 3242 6.119536 ACAAAGGTTCTAATGTTCTGTGTCA 58.880 36.000 0.00 0.00 0.00 3.58
3177 3243 6.619801 ACAAAGGTTCTAATGTTCTGTGTC 57.380 37.500 0.00 0.00 0.00 3.67
3224 3291 8.474006 AAACCAAATTTTTCACTAGTGTTGAC 57.526 30.769 21.99 0.00 0.00 3.18
3245 3312 5.047590 CACATCAAACCCTAAACCCTAAACC 60.048 44.000 0.00 0.00 0.00 3.27
3246 3313 5.566032 GCACATCAAACCCTAAACCCTAAAC 60.566 44.000 0.00 0.00 0.00 2.01
3247 3314 4.525100 GCACATCAAACCCTAAACCCTAAA 59.475 41.667 0.00 0.00 0.00 1.85
3248 3315 4.083565 GCACATCAAACCCTAAACCCTAA 58.916 43.478 0.00 0.00 0.00 2.69
3249 3316 3.332485 AGCACATCAAACCCTAAACCCTA 59.668 43.478 0.00 0.00 0.00 3.53
3250 3317 2.110011 AGCACATCAAACCCTAAACCCT 59.890 45.455 0.00 0.00 0.00 4.34
3251 3318 2.492088 GAGCACATCAAACCCTAAACCC 59.508 50.000 0.00 0.00 0.00 4.11
3331 3422 8.361889 CCACAATGAGATGGATATATTGCAAAA 58.638 33.333 1.71 0.00 38.34 2.44
3386 3481 9.594478 TCGCAAAGTGAATATATAAAAGTCTCA 57.406 29.630 0.00 0.00 0.00 3.27
3552 3647 3.242739 GGTACTCAACAACAACACAGCAG 60.243 47.826 0.00 0.00 0.00 4.24
3558 3653 3.376859 CAGCAAGGTACTCAACAACAACA 59.623 43.478 0.00 0.00 38.49 3.33
3738 3833 1.200020 GCAATGAGACCTTCCCAAACG 59.800 52.381 0.00 0.00 0.00 3.60
3760 3855 7.694886 AGCTTAATCTATTCAAACGTAAAGGC 58.305 34.615 0.00 0.00 0.00 4.35
4001 4096 5.186198 ACACAGCCCAACTTAAGACATATC 58.814 41.667 10.09 0.00 0.00 1.63
4009 4105 1.769026 TGCAACACAGCCCAACTTAA 58.231 45.000 0.00 0.00 0.00 1.85
4020 4116 3.305629 GCGAAACAAAGAAATGCAACACA 59.694 39.130 0.00 0.00 0.00 3.72
4053 4149 5.882040 TCAGATGGAGGTAGTACTATCCAG 58.118 45.833 23.28 14.02 44.67 3.86
4116 4212 6.642540 CGCTCAAACAGATGTATCTAGCATTA 59.357 38.462 11.84 0.00 34.68 1.90
4158 4255 2.362369 CCACCATCACGCTCCCTCT 61.362 63.158 0.00 0.00 0.00 3.69
4170 4267 1.825191 GCCATCGTGATGCCACCAT 60.825 57.895 4.29 0.00 40.12 3.55
4172 4269 0.463654 TAAGCCATCGTGATGCCACC 60.464 55.000 4.29 0.00 40.12 4.61
4263 4360 5.191727 TCTCCCATAAGCAGATTCCAAAA 57.808 39.130 0.00 0.00 0.00 2.44
4269 4366 6.443206 AGCAGTATATCTCCCATAAGCAGATT 59.557 38.462 0.00 0.00 0.00 2.40
4371 4469 1.003839 CCTAGCAACGCCACAAGGA 60.004 57.895 0.00 0.00 36.89 3.36
4386 4484 2.891580 AGACGTCAGAAACAAGAGCCTA 59.108 45.455 19.50 0.00 0.00 3.93
4408 4506 2.940410 TGTTTTCGGTGGTTCAGACTTC 59.060 45.455 0.00 0.00 0.00 3.01
4409 4507 2.993937 TGTTTTCGGTGGTTCAGACTT 58.006 42.857 0.00 0.00 0.00 3.01
4410 4508 2.702592 TGTTTTCGGTGGTTCAGACT 57.297 45.000 0.00 0.00 0.00 3.24
4411 4509 3.810941 TGTATGTTTTCGGTGGTTCAGAC 59.189 43.478 0.00 0.00 0.00 3.51
4432 4530 9.645059 CACAGTCCACAAGGAGTATAATATATG 57.355 37.037 0.00 0.00 46.04 1.78
4433 4531 8.816894 CCACAGTCCACAAGGAGTATAATATAT 58.183 37.037 0.00 0.00 46.04 0.86
4434 4532 8.008332 TCCACAGTCCACAAGGAGTATAATATA 58.992 37.037 0.00 0.00 46.04 0.86
4435 4533 6.844388 TCCACAGTCCACAAGGAGTATAATAT 59.156 38.462 0.00 0.00 46.04 1.28
4436 4534 6.199376 TCCACAGTCCACAAGGAGTATAATA 58.801 40.000 0.00 0.00 46.04 0.98
4437 4535 5.030147 TCCACAGTCCACAAGGAGTATAAT 58.970 41.667 0.00 0.00 46.04 1.28
4438 4536 4.422057 TCCACAGTCCACAAGGAGTATAA 58.578 43.478 0.00 0.00 46.04 0.98
4439 4537 4.023980 CTCCACAGTCCACAAGGAGTATA 58.976 47.826 0.00 0.00 46.04 1.47
4440 4538 2.834549 CTCCACAGTCCACAAGGAGTAT 59.165 50.000 0.00 0.00 46.04 2.12
4441 4539 2.248248 CTCCACAGTCCACAAGGAGTA 58.752 52.381 0.00 0.00 46.04 2.59
4443 4541 1.051812 ACTCCACAGTCCACAAGGAG 58.948 55.000 0.00 0.00 46.92 3.69
4444 4542 2.391926 TACTCCACAGTCCACAAGGA 57.608 50.000 0.00 0.00 43.21 3.36
4445 4543 4.020573 TGTTATACTCCACAGTCCACAAGG 60.021 45.833 0.00 0.00 33.62 3.61
4446 4544 5.147330 TGTTATACTCCACAGTCCACAAG 57.853 43.478 0.00 0.00 33.62 3.16
4447 4545 5.755409 ATGTTATACTCCACAGTCCACAA 57.245 39.130 0.00 0.00 33.62 3.33
4448 4546 6.860790 TTATGTTATACTCCACAGTCCACA 57.139 37.500 0.00 0.00 33.62 4.17
4449 4547 9.998106 ATTATTATGTTATACTCCACAGTCCAC 57.002 33.333 0.00 0.00 33.62 4.02
4490 4588 0.604780 CCTCAGGTTCTGCACACCAG 60.605 60.000 12.05 5.00 43.17 4.00
4539 4637 0.109597 GCTTCATCACGTTGGCCAAG 60.110 55.000 21.21 15.48 0.00 3.61
4545 4643 1.154413 GCACCGCTTCATCACGTTG 60.154 57.895 0.00 0.00 0.00 4.10
4731 4829 5.069781 ACACTAAGATTCTAGATCACCAGGC 59.930 44.000 0.00 0.00 0.00 4.85
4775 4885 4.403113 TCACTACATTAGCCATAACCGACA 59.597 41.667 0.00 0.00 0.00 4.35
4797 4907 0.811616 ATGAGACGAAGCGGGCATTC 60.812 55.000 0.00 0.00 0.00 2.67
4810 4920 6.484643 ACAAGGCATACATACAATGATGAGAC 59.515 38.462 0.00 0.00 0.00 3.36
4873 4983 2.703536 TGTCAGGCTCAACTAAACTCCA 59.296 45.455 0.00 0.00 0.00 3.86
4888 4999 1.997311 TGATCTGCCCCCTGTCAGG 60.997 63.158 12.40 12.40 34.30 3.86
4903 5015 3.511477 AGACTGTAAGACCACCTGTGAT 58.489 45.455 0.00 0.00 37.43 3.06
4920 5032 1.581954 CGCTTCAGACCACGAGACT 59.418 57.895 0.00 0.00 0.00 3.24
4966 5078 8.795786 TTTATTCACATTCTGCAAGTAAACAC 57.204 30.769 0.00 0.00 33.76 3.32
5065 5177 5.233476 TCAATACAACACAGACGAACACTTC 59.767 40.000 0.00 0.00 0.00 3.01
5089 5209 0.034756 TGCATGTTACCAGACACGCT 59.965 50.000 0.00 0.00 39.31 5.07
5096 5216 3.848272 AAAATCGGTGCATGTTACCAG 57.152 42.857 17.65 11.83 38.11 4.00
5104 5224 1.596408 GGGGCAAAAATCGGTGCAT 59.404 52.632 0.00 0.00 42.74 3.96
5142 5262 2.988839 GCCAGGCTGGGAAGGATGT 61.989 63.158 33.43 0.00 38.19 3.06
5166 5286 1.285641 CCACCGTGCATGTGTTTCC 59.714 57.895 15.54 0.00 31.71 3.13
5175 5295 1.679305 AACCAAACACCACCGTGCA 60.679 52.632 0.00 0.00 44.40 4.57
5196 5316 3.969287 TGCATCTGCTAGAACAAGTCT 57.031 42.857 3.53 0.00 42.66 3.24
5198 5318 4.392940 ACTTTGCATCTGCTAGAACAAGT 58.607 39.130 3.53 0.00 42.66 3.16
5204 5324 4.080919 ACCACATACTTTGCATCTGCTAGA 60.081 41.667 3.53 0.00 42.66 2.43
5205 5325 4.034858 CACCACATACTTTGCATCTGCTAG 59.965 45.833 3.53 3.91 42.66 3.42
5206 5326 3.940852 CACCACATACTTTGCATCTGCTA 59.059 43.478 3.53 0.00 42.66 3.49
5207 5327 2.751259 CACCACATACTTTGCATCTGCT 59.249 45.455 3.53 0.00 42.66 4.24
5221 5341 2.961741 TGCATGTAACCAAACACCACAT 59.038 40.909 0.00 0.00 30.75 3.21
5275 5395 4.344102 ACTCCGGCTTATGAGTTTATGCTA 59.656 41.667 0.00 0.00 38.67 3.49
5276 5396 3.134804 ACTCCGGCTTATGAGTTTATGCT 59.865 43.478 0.00 0.00 38.67 3.79
5277 5397 3.467803 ACTCCGGCTTATGAGTTTATGC 58.532 45.455 0.00 0.00 38.67 3.14
5278 5398 4.950050 AGACTCCGGCTTATGAGTTTATG 58.050 43.478 0.00 0.00 41.74 1.90
5279 5399 5.615925 AAGACTCCGGCTTATGAGTTTAT 57.384 39.130 0.00 0.00 41.74 1.40
5280 5400 6.534475 TTAAGACTCCGGCTTATGAGTTTA 57.466 37.500 0.00 0.00 41.74 2.01
5281 5401 3.983044 AAGACTCCGGCTTATGAGTTT 57.017 42.857 0.00 0.00 41.74 2.66
5306 5426 7.357303 GTGACCATTTTATCGTTTAACTGTGT 58.643 34.615 0.00 0.00 0.00 3.72
5309 5429 6.019152 CCGTGACCATTTTATCGTTTAACTG 58.981 40.000 0.00 0.00 0.00 3.16
5325 5445 0.179234 TTCAGACTTTGCCGTGACCA 59.821 50.000 0.00 0.00 0.00 4.02
5326 5446 1.002792 GTTTCAGACTTTGCCGTGACC 60.003 52.381 0.00 0.00 0.00 4.02
5330 5450 1.880027 GGATGTTTCAGACTTTGCCGT 59.120 47.619 0.00 0.00 0.00 5.68
5339 5459 6.240894 AGACTTTTGCATAGGATGTTTCAGA 58.759 36.000 0.00 0.00 0.00 3.27
5372 5492 7.340232 TGCCATGGATGCCTAAAATATTATCTC 59.660 37.037 18.40 0.00 0.00 2.75
5379 5499 4.344679 CCTTTGCCATGGATGCCTAAAATA 59.655 41.667 18.40 0.00 0.00 1.40
5436 5556 1.264826 TCTTCAACGACGACGATGTCA 59.735 47.619 15.32 3.47 41.70 3.58
5469 5589 2.847234 TGGCGACTCCCAACACCT 60.847 61.111 0.00 0.00 30.32 4.00
5473 5593 2.032681 AAGCTGGCGACTCCCAAC 59.967 61.111 0.00 0.00 33.73 3.77
5508 5628 2.289072 ACTGTTCACCAGATCAAGACCG 60.289 50.000 0.00 0.00 44.49 4.79
5510 5630 3.995199 TCACTGTTCACCAGATCAAGAC 58.005 45.455 0.00 0.00 44.49 3.01
5519 5639 1.073763 CCCCTTCATCACTGTTCACCA 59.926 52.381 0.00 0.00 0.00 4.17
5541 5661 3.195661 CTCGTGTTTGATAAGGGTAGGC 58.804 50.000 0.00 0.00 0.00 3.93
5544 5664 2.835764 AGGCTCGTGTTTGATAAGGGTA 59.164 45.455 0.00 0.00 0.00 3.69
5551 5671 0.322816 ATGGCAGGCTCGTGTTTGAT 60.323 50.000 0.00 0.00 0.00 2.57
5559 5679 0.873054 GATGATCAATGGCAGGCTCG 59.127 55.000 0.00 0.00 0.00 5.03
5561 5681 2.977580 TCTAGATGATCAATGGCAGGCT 59.022 45.455 0.00 0.00 0.00 4.58
5564 5684 3.244009 ACGGTCTAGATGATCAATGGCAG 60.244 47.826 0.00 0.00 0.00 4.85
5567 5687 4.302455 GTGACGGTCTAGATGATCAATGG 58.698 47.826 9.88 0.00 0.00 3.16
5568 5688 4.302455 GGTGACGGTCTAGATGATCAATG 58.698 47.826 9.88 0.00 0.00 2.82
5569 5689 3.322254 GGGTGACGGTCTAGATGATCAAT 59.678 47.826 9.88 0.00 0.00 2.57
5579 5699 1.255667 GCCTGAAGGGTGACGGTCTA 61.256 60.000 9.88 0.00 37.43 2.59
5602 5722 1.210155 GCTGATGACAAACACCGGC 59.790 57.895 0.00 0.00 37.23 6.13
5611 5731 4.259356 CAGAGGAATTCAAGCTGATGACA 58.741 43.478 7.93 0.00 0.00 3.58
5620 5740 3.009473 TCCTTGTCCCAGAGGAATTCAAG 59.991 47.826 7.93 0.00 46.38 3.02
5633 5753 3.019564 CCAATCACTTCATCCTTGTCCC 58.980 50.000 0.00 0.00 0.00 4.46
5638 5758 4.990526 AGTTCACCAATCACTTCATCCTT 58.009 39.130 0.00 0.00 0.00 3.36
5639 5759 4.042062 TGAGTTCACCAATCACTTCATCCT 59.958 41.667 0.00 0.00 0.00 3.24
5665 5785 2.401766 GGAGTGCCTGCCAATGTCG 61.402 63.158 0.00 0.00 0.00 4.35
5666 5786 1.303561 TGGAGTGCCTGCCAATGTC 60.304 57.895 0.00 0.00 34.31 3.06
5671 5791 1.529010 CAAACTGGAGTGCCTGCCA 60.529 57.895 0.00 0.00 36.65 4.92
5685 5805 4.178540 CAATGTCATCCTTGCATCCAAAC 58.821 43.478 0.00 0.00 0.00 2.93
5687 5807 2.166870 GCAATGTCATCCTTGCATCCAA 59.833 45.455 5.03 0.00 45.50 3.53


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.